modules/fcs_fcsgx
Run FCS-GX on assembled genomes. The contigs of the assembly are searched against a reference database excluding the given taxid.
Description
Run FCS-GX on assembled genomes. The contigs of the assembly are searched against a reference database excluding the given taxid.
Input
Files of the database downloaded from the ncbi server, https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/. All files of one db should be downloaded and given to the process as channel.collect(). The link contains 2 databases, test-only and all. Use all for pipeline usage and test-only for tests.
Tools
fcsUnited States Government Work
"The Foreign Contamination Screening (FCS) tool rapidly detects contaminants from foreign organisms in genome assemblies to prepare your data for submission. Therefore, the submission process to NCBI is faster and fewer contaminated genomes are submitted. This reduces errors in analyses and conclusions, not just for the original data submitter but for all subsequent users of the assembly."